staphscan

Tags: staphylococcus-aureus surveillance mlst spa-typing sccmec amr virulence sample-scope

Genome-based surveillance analysis of Staphylococcus aureus.

Uses StaphSCAN to perform genome-based surveillance of Staphylococcus aureus, integrating species identification, MLST, spa typing, SCCmec typing, capsular typing, and detection of virulence, biofilm, and antimicrobial resistance genes.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

db: Path?

Name	Type	Description
db	Path?	Custom MLST database directory

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Per-sample surveillance summary with MLST, spa type, SCCmec, capsule, AGR, resistance, biofilm, and virulence results
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

StaphSCAN Parameters

Parameter	Type	Default	Description
--staphscan_modules	string		Comma-separated list of modules to run
--staphscan_db_mlst	string	-	Path or tarball to custom MLST database

Used By

Subworkflows

• staphscan - Genome-based surveillance analysis of Staphylococcus aureus.

Workflows

• staphscan - Genome-based surveillance analysis of Staphylococcus aureus.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• StaphSCAN
  Bollini R StaphSCAN (v0.3.0). Zenodo (2026)

Source

View source on GitHub

Version

STAPHSCAN:
    - staphscan: 0.4.1